Dr. Susan S. Wallace
DNA Damage and Repair
Cells are constantly being assaulted by a wide variety of toxic agents in the environment. These agents damage cellular DNA and produce products which can result in cellular lethality, mutagenesis or carcinogenesis. An important class of damaging agents are highly reactive free radicals. Free radicals are produced by ionizing radiation, a variety of chemicals and most importantly, by normal cellular oxidative metabolism. Thus, free radical-induced damages are the most common cellular DNA lesions. In fact, it has been estimated that each day a cell receives on average about 10,000 oxidative hits. Since many of these damages have potential deleterious biological consequences, it is important to delineate how cells process these lesions. Since free radical-induced DNA damages are common lesions, cells have evolved efficient repair mechanisms to deal with them. The lesions are recognized by a battery of repair glycosylases and endonucleases which catalyze the first step in the base excision repair pathway. Recognition and removal of the damage are followed by repair polymerization and ligation. The enzymes involved in base excision repair are ubiquitous with homologs being found from bacteria to humans. If a lesion is not repaired prior to its encounter with the replication fork, the lesion is now capable of blocking replication, potentially causing cell death, or directing misinsertion of an incorrect base, leading to mutation and/or carcinogenesis. Since free radicals produce hundreds of different products in DNA, it is important to be able to assess which product is potentially deleterious, that is, which ones are potentially lethal and which ones are potentially mutagenic. Because free radical-inducing agents produce so many lesions in DNA all at the same time, it is difficult if not impossible to pinpoint cause/effect relationships of individual lesions. Our approach has been to select model representative products and introduce these either chemically or by using recombinant DNA technologies into substrate and biologically active DNA molecules and assessing their biological consequences. Once a lesion is either randomly or site specifically introduced into a DNA molecule, we can then ask if there are cellular enzymes present that recognize the lesion and remove it from DNA. Using this as well as in silico approaches, we have purified bacterial, viral, fungal and human enzymes that specifically recognize and remove oxidative DNA damages. Using mutants defective in these enzymes, in combination with biologically active DNA containing specific damages, we have defined cellular repair pathways. Our current efforts are focused on understanding the role that base excision repair processing plays in preventing mutations and lethal events in mammalian cells after they have been damaged by free radical producing agents. Recently, with Dr. Jeffrey Bond, we have been using bioinformatics to look at the evolution of the oxidative DNA glycosylases that recognize DNA base damages. In collaboration with both Drs. Bond and Doublié we are using biochemical and crystallographic approaches to determine the active site residues in these proteins that are responsible for substrate recognition.
In order to assess whether an unrepaired oxidative DNA lesion has potential biological consequence, we have introduced unique lesions into single-stranded template DNA molecules and asked whether these are blocks to DNA polymerases in vitro. If a lesion is a block to DNA polymerase, it is a potentially cytotoxic lesion. We have examined a number of oxidative lesions having a variety of structural characteristics and in every case, when a lesion was a block to DNA polymerase in vitro, it was also lethal when present in biologically active single-stranded transfecting DNA. We have used a similar approach to study the potential mutagenicity of individual oxidative DNA lesions by asking which base polymerases insert opposite a lesion in vitro, and then correlating these results with the mutagenic spectrum produced by each lesion in vivo. Thus far, the in vitro and in vivo results have been in good agreement. Very interestingly, we have been able to relate the ability of DNA polymerases to bypass individual lesions, as well as misinsertion direction by the particular lesion, to its mutagenic consequences in the cell. We have also found that the sequence context within which the lesion finds itself, is extremely important in misinsertion direction as well as lesion bypass. To understand the interactions between DNA polymerases and DNA lesions at the atomic level we are presently, in collaboration with Dr. Doublié, co-crystallizing lesion-containing oligonucleotides with DNA polymerases and have succeeded with two replication blocking damages, an abasic site and thymine glycol. In summary, our long-range goals include the elucidation of the repair processing and the mutagenic consequences of oxidative lesions in cellular DNA. We are employing chemical, enzymological, immunochemical, molecular biological, molecular genetic, bioinformatic and x-ray crystallographic techniques to answer these questions.
Liu M, Imamura K, Averill AM, Wallace SS, Doublié S. Structural Characterization of a Mouse Ortholog of Human NEIL3 with a Marked Preference for Single-Stranded DNA. Structure. 2013 Feb 5;21(2):247-256.
Wallace SS, Murphy DL, Sweasy JB. Base excision repair and cancer. Cancer Lett. 2012 Dec 31;327(1-2):73-89.
Liu M, Bandaru V, Bond JP, Jaruga P, Zhao X, Christov PP, Burrows CJ, Rizzo CJ, Dizdaroglu M, Wallace SS. The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivo. Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4925-30.
Dunn AR, Kad NM, Nelson SR, Warshaw DM, Wallace SS. Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA. Nucleic Acids Res. 2011 Sep 1;39(17):7487-7498.
Guo Y, Bandaru V, Jaruga P, Zhao X, Burrows CJ, Iwai S, Dizdaroglu M, Bond JP, <B>Wallace SS. The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts. DNA Repair (Amst). 2010 Feb 4;9(2):177-90.
Kathe SD, Barrantes-Reynolds R, Jaruga P, Newton MR, Burrows CJ, Bandaru V, Dizdaroglu M, Bond JP, Wallace SS. Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases. DNA Repair 2009 May 1;8(5):643-53.
Robey-Bond SM, Barrantes-Reynolds R, Bond JP, Wallace SS, Bandaru V. Clostridium acetobutylicum 8-oxoguanine DNA glycosylase (Ogg) differs from eukaryotic Oggs with respect to opposite base discrimination. Biochemistry. 2008 Jul 22;47(29):7626-36.
Bandaru V, Zhao X, Newton MR, Burrows CJ, Wallace SS. Human endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus. DNA Repair 2007 Nov;6(11):1629-41.
Yang N, Chaudhry MA, and Wallace SS. Base Excision Repair by hNTH1 and hOGG1: A Two Edged Sword in the Processing of DNA Damage in γ-irradiated Human Cells. DNA Repair. 2006 5(1):43-51.
Doublié S, Bandaru V, Bond JP, and Wallace, SS. The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity. Proc Natl Acad Sci U S A. 2004 101(28):10284-10289.